The Wii U and Nintendo 3DS have a huge redundancy issue to a point, where the systems are cannibalizing each other. By now both the Nintendo 3DS and Wii U share the same input configuration, they both have a touchscreen in addition to the main screen and in case of the New Nintendo 3DS even the exact same button layout. They also deal with 3D graphics most of the time. And both systems have a big handheld mentality, where the Wii U lets you play without a TV at any time. Handheld and console came very close to each other in this generation.

The result were many similar games for both systems. New Super Mario Bros. 2 and New Super Mario Bros. U, Super Mario 3D Land and Super Mario 3D World, Mario Kart 7 and Mario Kart 8, Super Smash Bros for Wii U and Super Smash Bros. for Nintendo 3DS, Hyrule Warriors and Hyrule Warriors: Legends... This list goes on and on and you can see the bigger scope very clearly in the above picture.

However, the Nintendo 3DS and especially the Nintendo 2DS are much cheaper and practical than the Wii U. Kids getting Nintendo systems from their parents is still an important income for Nintendo, but why should the parents buy their kids a Wii U, when a Nintendo 2DS does the same job just fine for a much smaller price? Just because the games look prettier and may offer different levels? There are only very few exclusive titles like Splatoon or Super Mario Maker on the Wii U, which aren't available in some form on 3DS, while the 3DS has a much stronger library including Pokémon and even exclusive Zelda games (something the Wii U won't offer until its demise).

At the same time Nintendo is essentially splitting their resources in half to make similar games for two different systems, while one systems eats away the other...

This is why I believe the rumors about the NX combining handheld and console in one system will be true. That somehow NX games will also be playable on the go with some external device. Games will be developed for "NX" and then simply be available for both home console and handheld devices. It would solve many issues with the current Nintendo.

Another approach would doing something very different on the handheld section, something simpler, more back to the roots, where the handheld is truly its own experience. We certainly didn't have such problems with the GameBoy. But I would suspect that Nintendo will try more on the Smartphone market instead.

Now, for The Legend of Zelda the division between handheld and console still has been going strong. Remakes and ports aside, classic topdown Zelda games appeared on the handheld and the big new 3rd Person Zelda games appear on the console. This way you get very unique experiences with Zelda on both systems. I always liked this approach and while I think it will be best for Nintendo to "merge" everything with the NX, I truly hope that this won't be the end of topdown Zelda.